I believe that when a warning "Letterspacing currently doesn't work with luatex" appears, it is true. I'm afraid there is nothing to answer here: it is a bug and the package maintainers clearly know about it. Even if they didn't, is was agreed that bug reports does not belong to TeX.SX.
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yo'Aug 10 '12 at 14:33

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Kerning is not yet enabled for the latest version of microtype (version 2.5) and luatex (version >=0.62). However, tracking should work if you use version 2.5 of microtype; this is one of the significant changes over version 2.4. However, version 2.5 is still in late-beta ('beta08' as of May 2012) and must be downloaded and installed by hand. You may obtain it from, e.g., tlcontrib.metatex.org/cgi-bin/package.cgi/action=view/id=608.
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MicoAug 10 '12 at 14:34

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tohecz: I took this example from a fairly recent TeX & friends posting where it appeared to work with LuaTeX, so I wanted to make sure it wasn't something funny about my setup that triggering this. I in no way indicated this as a "bug report". Mico: Thanks! In general: is there another way to handle letterspacing in LuaTeX?
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emacsomancerAug 10 '12 at 14:42

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@BeSlayed: Letterspacing and tracking should both work if you use version 2.5 of the microtype package and a version of lua(la)tex more recent than 0.62.
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MicoAug 10 '12 at 14:54

1 Answer
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If you use version 2.5 of the microtype package -- still in "late beta", but available online at http://tlcontrib.metatex.org/cgi-bin/package.cgi/action=view/id=608 -- you can use the letterspacing and tracking features of the package -- but not (yet) the kerning features; the latter are available only if the package is used with pdflatex.